my question was, with the yellow alert, are any changes to the basic marine navigation rules been made?

Answer 1

There have been no changes to the International Rules to Prevent Collision or COLREGS.
There have been many changes to commercial marine laws regarding notices of arrival and departure and security of water front property and vessels.

Answer 2

I not know of any changes.
You may browse around here;
http://www.navcen.uscg.gov/mwv/navrules/navrules.htm
The main thing is if you are to go outside America's coastal waters you may need a Passport to re-enter.

http://www.navcen.uscg.gov/lnm/default.htm
http://www.dhs.gov/xinfoshare/programs/Copy_of_press_release_0046.shtm